Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

ABSTRACT: The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.

SUBMITTER: Filho MA

PROVIDER: S-EPMC4880313 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

Filho Manoel A M MA Dutra José Diogo L JD Rocha Gerd B GB Simas Alfredo M AM Freire Ricardo O RO

PloS one 20160525 5

The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for yt ...[more]

PMID: 27223475

Similar Datasets

RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium.

Project description:The RM1 model for the lanthanides is parameterized for complexes of the trications of lanthanum, cerium, and praseodymium. The semiempirical quantum chemical model core stands for the [Xe]4fn electronic configuration, with n =0,1,2 for La(III), Ce(III), and Pr(III), respectively. In addition, the valence shell is described by three electrons in a set of 5d, 6s, and 6p orbitals. Results indicate that the present model is more accurate than the previous sparkle models, although these are still very good methods provided the ligands only possess oxygen or nitrogen atoms directly coordinated to the lanthanide ion. For all other different types of coordination, the present RM1 model for the lanthanides is much superior and must definitely be used. Overall, the accuracy of the model is of the order of 0.07Å for La(III) and Pr(III), and 0.08Å for Ce(III) for lanthanide-ligand atom distances which lie mostly around the 2.3Å to 2.6Å interval, implying an error around 3% only.

| S-EPMC4489505 | biostudies-literature

Highly near-IR emissive ytterbium(iii) complexes with unprecedented quantum yields.

Project description:The design of highly near-infrared (NIR) emissive lanthanide (Ln) complexes is challenging, owing to the lack of molecular systems with a high sensitization efficiency and the difficulty of achieving a large intrinsic quantum yield. Previous studies have reported success in optimizing individual factors and achieving high overall quantum yields, with the best yield being 12% for Yb(iii). Herein we report a series of highly NIR emissive Yb complexes, in which the Yb is sandwiched between an octafluorinated porphyrinate antenna ligand and a deuterated Kläui ligand, which allowed optimization of two factors in the same system, and one of the complexes had an unprecedented quantum yield of 63% (estimated uncertainty 15%) in CD2Cl2 with a long lifetime (?obs) of 714 ?s. Systematic analysis of the structure-photophysical properties relationship suggested that porphyrinates are effective antenna ligands with a sensitization efficiency up to ca. 100% and that replacement of the high-energy C-H oscillators in porphyrinate and Kläui ligands significantly improves the intrinsic quantum yield up to 75% (?obs/?rad), both of which contribute to enhancing the NIR emission intensity of Yb(iii) up to 25-fold. Besides the high luminescence efficiency, these Yb complexes have other attractive features such as excitation in the visible range and large extinction coefficients which make these Yb(iii) complexes outstanding optical materials in the NIR region.

| S-EPMC5480304 | biostudies-literature

Emergence of the super antenna effect in mixed crystals of ytterbium and lutetium complexes showing near-infrared luminescence.

Project description:The synthesis of luminescent molecular crystalline materials requires a good understanding of the luminescence properties of crystals in which many molecules are densely packed. Previously, we studied the near-infrared (NIR) luminescence of a trivalent ytterbium (Yb(iii)) complex with a Schiff base ligand, tris[2-(5-methylsalicylideneimino)ethyl]amine (H3L). Herein, we extended our study on the Yb complex (YbL) to enhance and understand its solid-state luminescence via mixed crystallization with the lutetium complex (LuL). We prepared (YbL) x (LuL)1-x mixed crystals (x = 0.01, 0.05, 0.1, 0.2, 0.3, 0.5, and 0.7) and studied their NIR luminescence properties. The NIR luminescence intensity per Yb(iii) ion for (YbL)0.01(LuL)0.99 was determined to be two orders of magnitude larger than that for YbL. The excitation spectral shape of (YbL)0.01(LuL)0.99 was different from the absorption spectral shape of YbL but similar to that of LuL. We attribute this observation to the emergence of an intermolecular energy-migration path. In the mixed crystals, LuL molecules acted as a light-harvesting super antenna for Yb(iii) luminescence. Decay measurements of the NIR luminescence for (YbL) x (LuL)1-x with x > 0.2 showed mono-exponential decay, while (YbL) x (LuL)1-x with x < 0.1 showed a grow-in component, which reflected the lifetime of the intermediate state for energy migration. The decay lifetime values tended to increase with decreasing x, suggesting that Yb(iii) isolation resulted in a reduction in concentration quenching. We propose that the luminescence enhancement in the highly Yb-diluted conditions was mainly caused by an increase in the super antenna effect.

| S-EPMC9597286 | biostudies-literature

Semiempirical quantum chemistry model for the lanthanides: RM1 (Recife Model 1) parameters for dysprosium, holmium and erbium.

Project description:Complexes of dysprosium, holmium, and erbium find many applications as single-molecule magnets, as contrast agents for magnetic resonance imaging, as anti-cancer agents, in optical telecommunications, etc. Therefore, the development of tools that can be proven helpful to complex design is presently an active area of research. In this article, we advance a major improvement to the semiempirical description of lanthanide complexes: the Recife Model 1, RM1, model for the lanthanides, parameterized for the trications of Dy, Ho, and Er. By representing such lanthanide in the RM1 calculation as a three-electron atom with a set of 5 d, 6 s, and 6 p semiempirical orbitals, the accuracy of the previous sparkle models, mainly concentrated on lanthanide-oxygen and lanthanide-nitrogen distances, is extended to other types of bonds in the trication complexes' coordination polyhedra, such as lanthanide-carbon, lanthanide-chlorine, etc. This is even more important as, for example, lanthanide-carbon atom distances in the coordination polyhedra of the complexes comprise about 30% of all distances for all complexes of Dy, Ho, and Er considered. Our results indicate that the average unsigned mean error for the lanthanide-carbon distances dropped from an average of 0.30 Å, for the sparkle models, to 0.04 Å for the RM1 model for the lanthanides; for a total of 509 such distances for the set of all Dy, Ho, and Er complexes considered. A similar behavior took place for the other distances as well, such as lanthanide-chlorine, lanthanide-bromine, lanthanide, phosphorus and lanthanide-sulfur. Thus, the RM1 model for the lanthanides, being advanced in this article, broadens the range of application of semiempirical models to lanthanide complexes by including comprehensively many other types of bonds not adequately described by the previous models.

| S-EPMC3908927 | biostudies-literature

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

Project description:We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

| S-EPMC6556433 | biostudies-literature

The Structures of ZnCl2-Ethanol Mixtures, a Spectroscopic and Quantum Chemical Calculation Study.

Project description:We report in this article the structural properties, spectral behavior and heterogeneity of ZnCl2-ethanol (EtOH) mixtures in a wide-composition range (1:3 to 1:14 in molar ratios), using ATR-FTIR spectroscopy and quantum chemical calculations. To improve the resolution of the initial IR spectra, excess spectroscopy and two-dimensional correlation spectroscopy were employed. The transformation process was suggested to be from EtOH trimer and EtOH tetramer to EtOH monomer, EtOH dimer and ZnCl2-3EtOH complex upon mixing. The theoretical findings showed that increasing the content of EtOH was accompanied with the flow of negative charge to ZnCl2. This led to reinforcement of the Zn←O coordination bonds, increase of the ionic character of Zn‒Cl bond and weakening and even dissociation of the Zn‒Cl bond. It was found that in some of the ZnCl2-EtOH complexes optimized at the gas phase or under the solvent effect, there existed hydroxyls with a very special interactive array in the form of Cl‒Zn+←O‒H…Cl-, which incredibly red-shifted to wavenumbers <3000 cm-1. This in-depth study shows the physical insights of the respective electrolyte alcoholic solutions, particularly the solvation process of the salt, help to rationalize the reported experimental results, and may shed light on understanding the properties of the deep eutectic solvents formed from ZnCl2 and an alcohol.

| S-EPMC8123294 | biostudies-literature

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters.

Project description:Semiempirical orthogonalization-corrected methods (OM1, OM2, and OM3) go beyond the standard MNDO model by explicitly including additional interactions into the Fock matrix in an approximate manner (Pauli repulsion, penetration effects, and core-valence interactions), which yields systematic improvements both for ground-state and excited-state properties. In this Article, we describe the underlying theoretical formalism of the OMx methods and their implementation in full detail, and we report all relevant OMx parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard set of mostly organic molecules commonly used in semiempirical method development, the OMx results are found to be superior to those from standard MNDO-type methods. Parametrized Grimme-type dispersion corrections can be added to OM2 and OM3 energies to provide a realistic treatment of noncovalent interaction energies, as demonstrated for the complexes in the S22 and S66×8 test sets.

| S-EPMC4785507 | biostudies-literature

Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules.

Project description:We introduce a fully stand-alone version of the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) program [S. Grimme, Angew. Chem. Int. Ed., 2013, 52, 6306] allowing efficient simulations for molecules composed of elements with atomic numbers up to Z = 86. The recently developed extended tight-binding semi-empirical method GFN-xTB has been combined with QCEIMS, thereby eliminating dependencies on third-party electronic structure software. Furthermore, for reasonable calculations of ionization potentials, as required by the method, a second tight-binding variant, IPEA-xTB, is introduced here. This novel combination of methods allows the automatic, fast and reasonably accurate computation of electron ionization mass spectra for structurally different molecules across the periodic table. In order to validate and inspect the transferability of the method, we perform large-scale simulations for some representative organic, organometallic, and main-group inorganic systems. Theoretical spectra for 23 molecules are compared directly to experimental data taken from standard databases. For the first time, realistic quantum chemistry based EI-MS for organometallic systems like ferrocene or copper(ii)acetylacetonate are presented. Compared to previously used semiempirical methods, GFN-xTB is faster, more robust, and yields overall higher quality spectra. The partially analysed theoretical reaction and fragmentation mechanisms are chemically reasonable and reveal in unprecedented detail the extreme complexity of high energy gas phase ion chemistry including complicated rearrangement reactions prior to dissociation.

| S-EPMC5603848 | biostudies-literature

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

Project description:In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.

| S-EPMC5952040 | biostudies-literature

The accuracy of quantum chemical methods for large noncovalent complexes.

Project description:We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable "accuracy/cost" ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent.

| S-EPMC3789125 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data